rs11088086

chr21-28736843-C-Achr21-28736843-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007067787.1(N6AMT1):n.936+85062G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 150,960 control chromosomes in the GnomAD database, including 6,081 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (6081 hom., cov: 31)
• Consequence: N6AMT1 XR_007067787.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

Genes affected

N6AMT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
N6AMT1	XR_007067787.1	n.936+85062G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41392 AN: 150882 Hom.: 6068 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.300

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.275 AC: 41450 AN: 150960 Hom.: 6081 Cov.: 31 AF XY: 0.271 AC XY: 19962 AN XY: 73662

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.301

Alfa AF: 0.133 Hom.: 269

Bravo AF: 0.295

Asia WGS AF: 0.324 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	2.2
Dann	Benign	0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11088086; hg19: chr21-30109165;